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  • Best reads normalization in RNA-Seq

    Hi, I'm analysing a bit of RNA-Seq data, in particular at the moment I try to compare the expression of genes in several conditions. To evaluate the expression value I used both FPKM value (Cufflinks v 1.3.0) and raw count (DESeq v 2.6). Due to the different number of reads of two samples (tipically about 10 million of reads!!), I suppose that I can't compare the value of a gene in this 2 samples; for example:

    FPKM_1=1 (or count_1=1) & FPKM=100 (or count_2=100) could not mean that there are differences between two condition (the difference is in order of size of one hundred).

    So, my question is: in the next step, do the software that perform differential analysis (like Cuffdiff or DESeq) allow for this difference?

    Otherwise, What's the best way to solve this problem?

    Thanks a lot.
    Mattia.
    Last edited by mattia; 04-17-2012, 05:50 AM.

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